library(ggpubr)
Loading required package: magrittr
Attaching package: ‘magrittr’
The following object is masked from ‘package:purrr’:
set_names
The following object is masked from ‘package:tidyr’:
extract
Attaching package: ‘ggpubr’
The following object is masked from ‘package:cowplot’:
get_legend
f74.rna.seu@meta.data <- f74.rna.seu@meta.data %>%
rownames_to_column("cell") %>%
left_join(annotation.df) %>%
column_to_rownames("cell")
Joining, by = "cell"
First I have made the snap file from the cellranger fragments.tsv file. Script is multiOmic_benchmark/preprocess/fragments2snap.sh.
Following integration vignette
Filtering based on number of reads per cell and ratio of fragments that are within promoters
barcode.ls = lapply(seq(snap.files), function(i){
barcodes = barcode.ls[[i]];
idx = which(
barcodes$logUMI >= cutoff.logUMI.low[i] &
barcodes$logUMI <= cutoff.logUMI.high[i] &
barcodes$promoter_ratio >= cutoff.FRIP.low[i] &
barcodes$promoter_ratio <= cutoff.FRIP.high[i]
);
barcodes[idx,]
});
x.sp.ls = lapply(seq(snap.files), function(i){
barcodes = barcode.ls[[i]];
x.sp = x.sp.ls[[i]];
barcode.shared = intersect(x.sp@barcode, barcodes$barcode);
x.sp = x.sp[match(barcode.shared, x.sp@barcode),];
barcodes = barcodes[match(barcode.shared, barcodes$barcode),];
x.sp@metaData = barcodes;
x.sp
})
names(x.sp.ls) = sample.names;
x.sp = Reduce(snapRbind, x.sp.ls);
x.sp@metaData["sample"] = x.sp@sample;
x.sp
number of barcodes: 6043
number of bins: 0
number of genes: 0
number of peaks: 0
number of motifs: 0
x.sp = addBmatToSnap(x.sp, bin.size = 5000)
Epoch: reading cell-bin count matrix session ...
Some items in the count matrix have abnormally high coverage perhaps due to the alignment errors. Therefore, we next remove top 0.1% items in the count matrix and then convert the remaining non-zero values to 1.
x.sp = makeBinary(x.sp, mat="bmat")
x.sp
number of barcodes: 6043
number of bins: 651791
number of genes: 0
number of peaks: 0
number of motifs: 0
Filter out bins overlapping w ENCODE blacklist
black_list = read.table("~/annotations/hg38.blacklist.bed.gz")
black_list.gr = GRanges(
black_list[,1],
IRanges(black_list[,2], black_list[,3])
);
idy = queryHits(
findOverlaps(x.sp@feature, black_list.gr)
);
if(length(idy) > 0){
x.sp = x.sp[,-idy, mat="bmat"];
};
x.sp
number of barcodes: 6043
number of bins: 651765
number of genes: 0
number of peaks: 0
number of motifs: 0
Exclude bad chromosomes
chr.exclude = seqlevels(x.sp@feature)[grep("random|chrM", seqlevels(x.sp@feature))]
idy = grep(paste(chr.exclude, collapse="|"), x.sp@feature)
if(length(idy) > 0){
x.sp = x.sp[,-idy, mat="bmat"]
}
x.sp
number of barcodes: 6043
number of bins: 650342
number of genes: 0
number of peaks: 0
number of motifs: 0
remove the top 5% bins that overlap with invariant features such as the house keeping gene promoters
bin.cov = log10(Matrix::colSums(x.sp@bmat)+1)
# bin.cov = Matrix::colSums(x.sp@bmat)
hist(
bin.cov[bin.cov > 0],
xlab="log10(bin cov)",
main="log10(Bin Cov)",
col="lightblue",
# xlim=c(0, 5),
breaks=100
);
bin.cutoff = quantile(bin.cov[bin.cov > 0], 0.95)
idy = which(bin.cov <= bin.cutoff & bin.cov > 0)
x.sp = x.sp[, idy, mat="bmat"];
x.sp
number of barcodes: 6043
number of bins: 539584
number of genes: 0
number of peaks: 0
number of motifs: 0
Remove any cells of bin coverage less than 1,000. The rational behind this is that some cells may have high number of unique fragments but end up with low bin coverage after filtering. This step is optional but highly recommanded.
idx = which(Matrix::rowSums(x.sp@bmat) > 1000);
x.sp = x.sp[idx,];
x.sp
number of barcodes: 5793
number of bins: 539584
number of genes: 0
number of peaks: 0
number of motifs: 0
Uses diffusion map algorithm w sampling technique to make it fast.
## Sample 100 cells as landmarks
row.covs.dens <- density(
x = x.sp@metaData[,"logUMI"],
bw = 'nrd', adjust = 1
)
sampling_prob <- 1 / (approx(x = row.covs.dens$x, y = row.covs.dens$y, xout = x.sp@metaData[,"logUMI"])$y + .Machine$double.eps);
set.seed(1)
idx.landmark.ds <- sort(sample(x = seq(nrow(x.sp)), size = 1000, prob = sampling_prob))
## Split between landmark and query cells
x.landmark.sp = x.sp[idx.landmark.ds,];
x.query.sp = x.sp[-idx.landmark.ds,];
## Run diffusion map on landmark
x.landmark.sp = runDiffusionMaps(
obj= x.landmark.sp,
input.mat="bmat",
num.eigs=50
);
Epoch: checking the inputs ...
Epoch: computing jaccard similarity matrix ...
Epoch: fitting regression model ...
Epoch: performing normalization ...
Epoch: computing eigen decomposition ...
Epoch: Done
x.landmark.sp@metaData$landmark = 1;
## Project query cells
x.query.sp = runDiffusionMapsExtension(
obj1=x.landmark.sp,
obj2=x.query.sp,
input.mat="bmat"
)
Epoch: checking the inputs ...
Epoch: computing jaccard similarity matrix ...
Epoch: performing normalization ...
Epoch: projecting query cells to the reference ...
Epoch: Done
x.query.sp@metaData$landmark = 0;
## Combine
x.sp = snapRbind(x.landmark.sp, x.query.sp);
'rBind' is deprecated.
Since R version 3.2.0, base's rbind() should work fine with S4 objects
x.sp = x.sp[order(x.sp@metaData[,"sample"])]; #IMPORTANT
To determine significant diffusion components: > We use an ad hoc method by simply looking at a pairwise plot and select the number of eigen vectors that the scatter plot starts looking like a blob. In the below example, we choose the first 15 eigen vectors.
plotDimReductPW(
obj=x.sp,
eigs.dims=1:50,
point.size=0.3,
point.color="grey",
point.shape=19,
point.alpha=0.6,
down.sample=5000,
pdf.file.name=NULL,
pdf.height=7,
pdf.width=7
);
x.sp=runCluster(
obj=x.sp,
tmp.folder=tempdir(),
louvain.lib="leiden",
seed.use=10,
resolution=0.7
);
Epoch: checking input parameters
Epoch: finding clusters using leiden
Visualization
x.sp <- readRDS( "~/my_data/cellranger-atac110_count_30439_WSSS8038360_GRCh38-1_1_0.snapATAC.RDS")
Loading required package: SnapATAC
Loading required package: rhdf5
Attaching package: ‘SnapATAC’
The following object is masked from ‘package:liger’:
plotGene
Repeat visualization on gmat
FeaturePlot(f74.seu, features = c('PTPRC','CD4','CD8A','CD8B','CD79A','FOXN1','EPCAM','PDGFRA','GNG4', 'FOXP3','RAG1','RAG2','NKG7','CCR7'), reduction = "umap.snap")
All cells have the same value (0) of CD79A.All cells have the same value (0) of RAG2.All cells have the same value (0) of NKG7.All cells have the same value (0) of CCR7.
DimHeatmap(f74.seu, dims = 1:6, balanced = TRUE,ncol = 1)
31 Oct 2019 09:28:40 [rsession-] CLIENT EXCEPTION (rsession-jovyan): (TypeError) : Cannot read property 'a' of null;
org/rstudio/studio/client/workbench/views/source/editors/text/ChunkPlotPage.java#52::execute
org/rstudio/studio/client/workbench/views/source/editors/text/ChunkPlotWidget.java#49::onBrowserEvent
com/google/gwt/user/client/DOM.java#1414::dispatchEvent
com/google/gwt/user/client/impl/DOMImplStandard.java#312::dispatchEvent
com/google/gwt/user/client/impl/DOMImplStandard.java#334::dispatchUnhandledEvent
com/google/gwt/core/client/impl/Impl.java#244::apply
com/google/gwt/core/client/impl/Impl.java#283::entry0
rstudio-0.js#-1::eval
Client-ID: 7beb3877-891d-4e16-98d5-f8cca1f72d5d
User-Agent: Mozilla/5.0 (Macintosh Intel Mac OS X 10_14_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/77.0.3865.90 Safari/537.36
DAGs_cl <- FindAllMarkers(f74.seu, min.pct = 0.2, logfc.threshold = 0.3)
Calculating cluster 1
| | 0 % ~calculating
|++++ | 7 % ~02s
|+++++++ | 13% ~02s
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s
Calculating cluster 2
| | 0 % ~calculating
|+ | 1 % ~36s
|++ | 2 % ~33s
|++ | 4 % ~31s
|+++ | 5 % ~30s
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|++++++++++++++++++++++++++++++++ | 64% ~12s
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|+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=27s
Calculating cluster 3
| | 0 % ~calculating
|+ | 1 % ~24s
|++ | 2 % ~24s
|++ | 3 % ~24s
|+++ | 4 % ~24s
|+++ | 6 % ~23s
|++++ | 7 % ~23s
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|++++++++++++++++++++++++++++++ | 59% ~10s
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=27s
Calculating cluster 4
| | 0 % ~calculating
|+ | 2 % ~02s
|++ | 4 % ~02s
|+++ | 5 % ~02s
|++++ | 7 % ~02s
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=03s
Calculating cluster 5
| | 0 % ~calculating
|+ | 1 % ~07s
|++ | 3 % ~07s
|++ | 4 % ~07s
|+++ | 5 % ~07s
|++++ | 7 % ~07s
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=07s
Calculating cluster 6
| | 0 % ~calculating
|+ | 1 % ~13s
|++ | 2 % ~14s
|++ | 3 % ~14s
|+++ | 4 % ~13s
|+++ | 5 % ~13s
|++++ | 6 % ~13s
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|+++++++++++++++++++++++++++++++++++++++++ | 81% ~03s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~02s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 84% ~02s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~02s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 88% ~02s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~01s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=13s
Calculating cluster 7
| | 0 % ~calculating
|+ | 1 % ~02m 24s
|++ | 2 % ~02m 23s
|++ | 3 % ~02m 20s
|+++ | 4 % ~02m 18s
|+++ | 5 % ~02m 15s
|++++ | 6 % ~02m 12s
|++++ | 7 % ~02m 29s
|+++++ | 8 % ~02m 24s
|+++++ | 9 % ~02m 20s
|++++++ | 10% ~02m 17s
|++++++ | 11% ~02m 14s
|+++++++ | 12% ~02m 11s
|+++++++ | 13% ~02m 09s
|++++++++ | 14% ~02m 06s
|++++++++ | 15% ~02m 04s
|+++++++++ | 16% ~02m 02s
|+++++++++ | 17% ~01m 60s
|++++++++++ | 18% ~01m 58s
|++++++++++ | 19% ~01m 56s
|+++++++++++ | 20% ~01m 54s
|+++++++++++ | 21% ~01m 53s
|++++++++++++ | 22% ~01m 51s
|++++++++++++ | 23% ~01m 49s
|+++++++++++++ | 24% ~01m 47s
|+++++++++++++ | 25% ~01m 45s
|++++++++++++++ | 26% ~01m 43s
|++++++++++++++ | 27% ~01m 42s
|+++++++++++++++ | 28% ~01m 40s
|+++++++++++++++ | 29% ~01m 39s
|++++++++++++++++ | 30% ~01m 37s
|++++++++++++++++ | 31% ~01m 35s
|+++++++++++++++++ | 32% ~01m 34s
|+++++++++++++++++ | 33% ~01m 32s
|++++++++++++++++++ | 34% ~01m 31s
|++++++++++++++++++ | 35% ~01m 29s
|+++++++++++++++++++ | 36% ~01m 31s
|+++++++++++++++++++ | 37% ~01m 29s
|++++++++++++++++++++ | 38% ~01m 28s
|++++++++++++++++++++ | 39% ~01m 26s
|+++++++++++++++++++++ | 40% ~01m 25s
|+++++++++++++++++++++ | 41% ~01m 23s
|++++++++++++++++++++++ | 42% ~01m 22s
|++++++++++++++++++++++ | 43% ~01m 20s
|+++++++++++++++++++++++ | 44% ~01m 19s
|+++++++++++++++++++++++ | 45% ~01m 17s
|++++++++++++++++++++++++ | 46% ~01m 15s
|++++++++++++++++++++++++ | 47% ~01m 14s
|+++++++++++++++++++++++++ | 48% ~01m 12s
|+++++++++++++++++++++++++ | 49% ~01m 11s
|++++++++++++++++++++++++++ | 51% ~01m 09s
|++++++++++++++++++++++++++ | 52% ~01m 08s
|+++++++++++++++++++++++++++ | 53% ~01m 06s
|+++++++++++++++++++++++++++ | 54% ~01m 05s
|++++++++++++++++++++++++++++ | 55% ~01m 03s
|++++++++++++++++++++++++++++ | 56% ~01m 02s
|+++++++++++++++++++++++++++++ | 57% ~01m 00s
|+++++++++++++++++++++++++++++ | 58% ~59s
|++++++++++++++++++++++++++++++ | 59% ~01m 04s
|++++++++++++++++++++++++++++++ | 60% ~01m 03s
|+++++++++++++++++++++++++++++++ | 61% ~01m 01s
|+++++++++++++++++++++++++++++++ | 62% ~59s
|++++++++++++++++++++++++++++++++ | 63% ~57s
|++++++++++++++++++++++++++++++++ | 64% ~56s
|+++++++++++++++++++++++++++++++++ | 65% ~54s
|+++++++++++++++++++++++++++++++++ | 66% ~52s
|++++++++++++++++++++++++++++++++++ | 67% ~51s
|++++++++++++++++++++++++++++++++++ | 68% ~49s
|+++++++++++++++++++++++++++++++++++ | 69% ~47s
|+++++++++++++++++++++++++++++++++++ | 70% ~46s
|++++++++++++++++++++++++++++++++++++ | 71% ~44s
|++++++++++++++++++++++++++++++++++++ | 72% ~42s
|+++++++++++++++++++++++++++++++++++++ | 73% ~41s
|+++++++++++++++++++++++++++++++++++++ | 74% ~39s
|++++++++++++++++++++++++++++++++++++++ | 75% ~38s
|++++++++++++++++++++++++++++++++++++++ | 76% ~36s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~34s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~33s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~31s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~30s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~28s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~27s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~25s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~24s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~22s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~21s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~19s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~18s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~16s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~15s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~13s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~12s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~10s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~09s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~07s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~06s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~04s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~03s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 22s
Calculating cluster 8
| | 0 % ~calculating
|+ | 1 % ~01m 34s
|++ | 2 % ~01m 32s
|++ | 3 % ~01m 34s
|+++ | 4 % ~01m 32s
|+++ | 5 % ~01m 59s
|++++ | 6 % ~01m 53s
|++++ | 7 % ~01m 48s
|+++++ | 8 % ~01m 45s
|+++++ | 9 % ~01m 41s
|++++++ | 10% ~01m 38s
|++++++ | 11% ~01m 36s
|+++++++ | 12% ~01m 34s
|+++++++ | 13% ~01m 32s
|++++++++ | 14% ~01m 30s
|++++++++ | 15% ~01m 28s
|+++++++++ | 16% ~01m 27s
|+++++++++ | 17% ~01m 25s
|++++++++++ | 18% ~01m 24s
|++++++++++ | 19% ~01m 23s
|+++++++++++ | 20% ~01m 21s
|+++++++++++ | 21% ~01m 20s
|++++++++++++ | 22% ~01m 19s
|++++++++++++ | 23% ~01m 17s
|+++++++++++++ | 24% ~01m 16s
|+++++++++++++ | 26% ~01m 15s
|++++++++++++++ | 27% ~01m 14s
|++++++++++++++ | 28% ~01m 12s
|+++++++++++++++ | 29% ~01m 11s
|+++++++++++++++ | 30% ~01m 10s
|++++++++++++++++ | 31% ~01m 09s
|++++++++++++++++ | 32% ~01m 08s
|+++++++++++++++++ | 33% ~01m 07s
|+++++++++++++++++ | 34% ~01m 06s
|++++++++++++++++++ | 35% ~01m 05s
|++++++++++++++++++ | 36% ~01m 04s
|+++++++++++++++++++ | 37% ~01m 03s
|+++++++++++++++++++ | 38% ~01m 02s
|++++++++++++++++++++ | 39% ~01m 00s
|++++++++++++++++++++ | 40% ~59s
|+++++++++++++++++++++ | 41% ~58s
|+++++++++++++++++++++ | 42% ~57s
|++++++++++++++++++++++ | 43% ~56s
|++++++++++++++++++++++ | 44% ~55s
|+++++++++++++++++++++++ | 45% ~54s
|+++++++++++++++++++++++ | 46% ~53s
|++++++++++++++++++++++++ | 47% ~52s
|++++++++++++++++++++++++ | 48% ~51s
|+++++++++++++++++++++++++ | 49% ~50s
|+++++++++++++++++++++++++ | 50% ~49s
|++++++++++++++++++++++++++ | 51% ~48s
|+++++++++++++++++++++++++++ | 52% ~47s
|+++++++++++++++++++++++++++ | 53% ~46s
|++++++++++++++++++++++++++++ | 54% ~45s
|++++++++++++++++++++++++++++ | 55% ~44s
|+++++++++++++++++++++++++++++ | 56% ~43s
|+++++++++++++++++++++++++++++ | 57% ~42s
|++++++++++++++++++++++++++++++ | 58% ~41s
|++++++++++++++++++++++++++++++ | 59% ~40s
|+++++++++++++++++++++++++++++++ | 60% ~39s
|+++++++++++++++++++++++++++++++ | 61% ~38s
|++++++++++++++++++++++++++++++++ | 62% ~37s
|++++++++++++++++++++++++++++++++ | 63% ~36s
|+++++++++++++++++++++++++++++++++ | 64% ~35s
|+++++++++++++++++++++++++++++++++ | 65% ~34s
|++++++++++++++++++++++++++++++++++ | 66% ~33s
|++++++++++++++++++++++++++++++++++ | 67% ~33s
|+++++++++++++++++++++++++++++++++++ | 68% ~32s
|+++++++++++++++++++++++++++++++++++ | 69% ~31s
|++++++++++++++++++++++++++++++++++++ | 70% ~30s
|++++++++++++++++++++++++++++++++++++ | 71% ~28s
|+++++++++++++++++++++++++++++++++++++ | 72% ~27s
|+++++++++++++++++++++++++++++++++++++ | 73% ~26s
|++++++++++++++++++++++++++++++++++++++ | 74% ~25s
|++++++++++++++++++++++++++++++++++++++ | 76% ~24s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~23s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~22s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~21s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~20s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~19s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~18s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~17s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~16s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~15s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~14s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~13s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~12s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~11s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~10s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~09s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~08s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~07s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~06s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~05s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~04s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~03s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 39s
Calculating cluster 9
| | 0 % ~calculating
|+ | 1 % ~01m 35s
|+ | 2 % ~01m 35s
|++ | 3 % ~01m 33s
|++ | 4 % ~01m 34s
|+++ | 5 % ~01m 33s
|+++ | 6 % ~01m 31s
|++++ | 7 % ~01m 29s
|++++ | 8 % ~01m 28s
|+++++ | 9 % ~01m 27s
|+++++ | 10% ~01m 26s
|++++++ | 11% ~01m 26s
|++++++ | 12% ~01m 24s
|+++++++ | 13% ~01m 23s
|+++++++ | 14% ~01m 22s
|++++++++ | 15% ~01m 21s
|++++++++ | 16% ~01m 20s
|+++++++++ | 17% ~01m 19s
|+++++++++ | 18% ~01m 19s
|++++++++++ | 19% ~01m 18s
|++++++++++ | 20% ~01m 16s
|+++++++++++ | 21% ~01m 16s
|+++++++++++ | 22% ~01m 15s
|++++++++++++ | 23% ~01m 14s
|++++++++++++ | 24% ~01m 13s
|+++++++++++++ | 25% ~01m 12s
|+++++++++++++ | 26% ~01m 11s
|++++++++++++++ | 27% ~01m 10s
|++++++++++++++ | 28% ~01m 09s
|+++++++++++++++ | 29% ~01m 08s
|+++++++++++++++ | 30% ~01m 07s
|++++++++++++++++ | 31% ~01m 06s
|++++++++++++++++ | 32% ~01m 05s
|+++++++++++++++++ | 33% ~01m 04s
|+++++++++++++++++ | 34% ~01m 03s
|++++++++++++++++++ | 35% ~01m 02s
|++++++++++++++++++ | 36% ~01m 01s
|+++++++++++++++++++ | 37% ~01m 00s
|+++++++++++++++++++ | 38% ~59s
|++++++++++++++++++++ | 39% ~58s
|++++++++++++++++++++ | 40% ~57s
|+++++++++++++++++++++ | 41% ~56s
|+++++++++++++++++++++ | 42% ~58s
|++++++++++++++++++++++ | 43% ~57s
|++++++++++++++++++++++ | 44% ~56s
|+++++++++++++++++++++++ | 45% ~55s
|+++++++++++++++++++++++ | 46% ~54s
|++++++++++++++++++++++++ | 47% ~52s
|++++++++++++++++++++++++ | 48% ~51s
|+++++++++++++++++++++++++ | 49% ~50s
|+++++++++++++++++++++++++ | 50% ~49s
|++++++++++++++++++++++++++ | 51% ~48s
|++++++++++++++++++++++++++ | 52% ~47s
|+++++++++++++++++++++++++++ | 53% ~46s
|+++++++++++++++++++++++++++ | 54% ~45s
|++++++++++++++++++++++++++++ | 55% ~44s
|++++++++++++++++++++++++++++ | 56% ~43s
|+++++++++++++++++++++++++++++ | 57% ~42s
|+++++++++++++++++++++++++++++ | 58% ~41s
|++++++++++++++++++++++++++++++ | 59% ~40s
|++++++++++++++++++++++++++++++ | 60% ~39s
|+++++++++++++++++++++++++++++++ | 61% ~38s
|+++++++++++++++++++++++++++++++ | 62% ~37s
|++++++++++++++++++++++++++++++++ | 63% ~36s
|++++++++++++++++++++++++++++++++ | 64% ~35s
|+++++++++++++++++++++++++++++++++ | 65% ~34s
|+++++++++++++++++++++++++++++++++ | 66% ~33s
|++++++++++++++++++++++++++++++++++ | 67% ~32s
|++++++++++++++++++++++++++++++++++ | 68% ~31s
|+++++++++++++++++++++++++++++++++++ | 69% ~30s
|+++++++++++++++++++++++++++++++++++ | 70% ~29s
|++++++++++++++++++++++++++++++++++++ | 71% ~28s
|++++++++++++++++++++++++++++++++++++ | 72% ~27s
|+++++++++++++++++++++++++++++++++++++ | 73% ~26s
|+++++++++++++++++++++++++++++++++++++ | 74% ~25s
|++++++++++++++++++++++++++++++++++++++ | 75% ~25s
|++++++++++++++++++++++++++++++++++++++ | 76% ~24s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~23s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~22s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~21s
|++++++++++++++++++++++++++++++++++++++++ | 80% ~20s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~19s
|+++++++++++++++++++++++++++++++++++++++++ | 82% ~18s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~17s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~16s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~15s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~14s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~13s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~12s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~11s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~10s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~09s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~08s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~07s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~06s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~05s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~04s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~03s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~01s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 39s
Calculating cluster 10
| | 0 % ~calculating
|+ | 1 % ~02m 55s
|++ | 2 % ~02m 47s
|++ | 3 % ~02m 43s
|+++ | 4 % ~02m 40s
|+++ | 5 % ~02m 37s
|++++ | 6 % ~02m 34s
|++++ | 7 % ~02m 33s
|+++++ | 8 % ~02m 31s
|+++++ | 9 % ~02m 28s
|++++++ | 10% ~02m 27s
|++++++ | 11% ~02m 25s
|+++++++ | 12% ~02m 22s
|+++++++ | 13% ~02m 20s
|++++++++ | 14% ~02m 18s
|++++++++ | 15% ~02m 17s
|+++++++++ | 16% ~02m 15s
|+++++++++ | 18% ~02m 13s
|++++++++++ | 19% ~02m 18s
|++++++++++ | 20% ~02m 16s
|+++++++++++ | 21% ~02m 14s
|+++++++++++ | 22% ~02m 12s
|++++++++++++ | 23% ~02m 10s
|++++++++++++ | 24% ~02m 08s
|+++++++++++++ | 25% ~02m 06s
|+++++++++++++ | 26% ~02m 04s
|++++++++++++++ | 27% ~02m 02s
|++++++++++++++ | 28% ~01m 60s
|+++++++++++++++ | 29% ~01m 58s
|+++++++++++++++ | 30% ~01m 56s
|++++++++++++++++ | 31% ~01m 54s
|++++++++++++++++ | 32% ~01m 52s
|+++++++++++++++++ | 33% ~01m 50s
|++++++++++++++++++ | 34% ~01m 49s
|++++++++++++++++++ | 35% ~01m 47s
|+++++++++++++++++++ | 36% ~01m 45s
|+++++++++++++++++++ | 37% ~01m 43s
|++++++++++++++++++++ | 38% ~01m 42s
|++++++++++++++++++++ | 39% ~01m 40s
|+++++++++++++++++++++ | 40% ~01m 38s
|+++++++++++++++++++++ | 41% ~01m 37s
|++++++++++++++++++++++ | 42% ~01m 37s
|++++++++++++++++++++++ | 43% ~01m 35s
|+++++++++++++++++++++++ | 44% ~01m 34s
|+++++++++++++++++++++++ | 45% ~01m 32s
|++++++++++++++++++++++++ | 46% ~01m 30s
|++++++++++++++++++++++++ | 47% ~01m 28s
|+++++++++++++++++++++++++ | 48% ~01m 26s
|+++++++++++++++++++++++++ | 49% ~01m 25s
|++++++++++++++++++++++++++ | 51% ~01m 23s
|++++++++++++++++++++++++++ | 52% ~01m 21s
|+++++++++++++++++++++++++++ | 53% ~01m 19s
|+++++++++++++++++++++++++++ | 54% ~01m 18s
|++++++++++++++++++++++++++++ | 55% ~01m 16s
|++++++++++++++++++++++++++++ | 56% ~01m 14s
|+++++++++++++++++++++++++++++ | 57% ~01m 12s
|+++++++++++++++++++++++++++++ | 58% ~01m 11s
|++++++++++++++++++++++++++++++ | 59% ~01m 09s
|++++++++++++++++++++++++++++++ | 60% ~01m 07s
|+++++++++++++++++++++++++++++++ | 61% ~01m 08s
|+++++++++++++++++++++++++++++++ | 62% ~01m 06s
|++++++++++++++++++++++++++++++++ | 63% ~01m 04s
|++++++++++++++++++++++++++++++++ | 64% ~01m 02s
|+++++++++++++++++++++++++++++++++ | 65% ~01m 01s
|+++++++++++++++++++++++++++++++++ | 66% ~59s
|++++++++++++++++++++++++++++++++++ | 67% ~57s
|+++++++++++++++++++++++++++++++++++ | 68% ~55s
|+++++++++++++++++++++++++++++++++++ | 69% ~53s
|++++++++++++++++++++++++++++++++++++ | 70% ~51s
|++++++++++++++++++++++++++++++++++++ | 71% ~50s
|+++++++++++++++++++++++++++++++++++++ | 72% ~48s
|+++++++++++++++++++++++++++++++++++++ | 73% ~46s
|++++++++++++++++++++++++++++++++++++++ | 74% ~44s
|++++++++++++++++++++++++++++++++++++++ | 75% ~42s
|+++++++++++++++++++++++++++++++++++++++ | 76% ~41s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~39s
|++++++++++++++++++++++++++++++++++++++++ | 78% ~37s
|++++++++++++++++++++++++++++++++++++++++ | 79% ~38s
|+++++++++++++++++++++++++++++++++++++++++ | 80% ~36s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~34s
|++++++++++++++++++++++++++++++++++++++++++ | 82% ~32s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~30s
|+++++++++++++++++++++++++++++++++++++++++++ | 85% ~28s
|+++++++++++++++++++++++++++++++++++++++++++ | 86% ~26s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~24s
|++++++++++++++++++++++++++++++++++++++++++++ | 88% ~22s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~20s
|+++++++++++++++++++++++++++++++++++++++++++++ | 90% ~19s
|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~17s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~15s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 93% ~13s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~11s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95% ~09s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~07s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~06s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 98% ~04s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~02s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 57s
DAGs_cl <-
DAGs_cl %>%
mutate(positive=avg_logFC > 0)
top10_markers <- DAGs_cl %>%
filter(positive) %>%
group_by(cluster) %>%
arrange(p_val_adj) %>%
top_n(10) %>%
pull(gene) %>%
unique()
Selecting by positive
top10_markers <- DAGs_cl %>%
filter(positive) %>%
group_by(cluster) %>%
# arrange(p_val_adj) %>%
top_n(10,wt = - p_val_adj) %>%
pull(gene)
DotPlot(f74.seu, features = top10_markers) +
coord_flip()
Expression of markers in RNA data
map(1:10, ~ plot_cluster_marker_ATACvsRNA(.x))
All cells have the same value (0) of MIR4300HG.All cells have the same value (0) of NOS1.All cells have the same value (0) of RPH3A.Cannot convert object of class listggarrange into a grob.All cells have the same value (0) of C5orf66-AS2.All cells have the same value (0) of CYP3A43.
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]
[[10]]
Only between cluster 1 and 2